Zeta
by The Laugh Master
Summary: No one knows the Doctor better than the ship he's been traveling with for hundreds of years. But the Doctor never understood quite how well his TARDIS knew him until she starts acting strangely, and he needs travel a long ways inside the ship to fix her. Amy and Rory find out things about the Doctor's past that he hasn't told them. Small cameos from many past New Who companions!
1. Chapter 1

**Disclaimer: I don't own anything Doctor Who**

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The Doctor had been having a wonderful time, a really quite lovely day, before the ringing started.

He had decided to take Amy and Rory to Zeta Madrigal Dash Aquamarine – Nine, a charming little floating obelisk in the middle of the Eagle Nebula. They had just come around the corner of one little street in the underground marketplace they'd been exploring when they heard it.

"Doctor, do you hear that?" Amy asked curiously, peering around a fruit vendors stall.

"Ah, Singing Squashies!" The Doctor exclaimed delightedly, and picked up a round lavender-colored fruit the size of a ping pong ball and gave it a sniff. It was emitting a quiet tingling sound, like bells that were trying to talk.

"Singing _Squashies?_" Rory asked skeptically.

"Yup!" said The Doctor, swinging around, showing the small fruit to him, "Singing fruit! Not actually singing, of course, but filled with little tiny seeds that bounce around inside it when it gets hot. And tastes like the ocean! Earth oceans, of course, not the ones around here, _they_ all taste like strawberries. Yuck." The Doctor pulled a face and stuck his tongue out.

"What's wrong with strawberries?" Rory asked.

"Rory, Rory, Rory," The Doctor said, shaking his head and tossing the singing squashy back on the basket where he'd gotten it from, where the vendor, a bug-eyed humanoid, bubbled at them and tugged the basket closer. "_Everything_'s wrong with strawberries."

"Let me guess, _you_ just don't like them."

"Doctor, it's not that, I hear something else." Amy said from a few paces forward, looking all around.

"What?" The Doctor asked, coming up from behind. He leaped casually over an overturned bin and stood very still, listening. "Yeah… I hear it too." He looked confused.

"It _sounds_ like a phone," The Doctor said, holding up a finger, "_Except_ Zeta Madrigal Dash Aquamarine – Nine doesn't _have _phones."

"Well, it's not me," Rory offered, checking his cell phone that The Doctor had set up to receive signal all across the universe.

"No, it isn't, it's coming from up ahead," The Doctor said quietly, staring down the path. "Funny 'cause that's right near where I parked the…" He stopped, eyes growing wide. "Oh no." he said very quietly "Oh no no no _no!_" He took off at a run and the Ponds came tearing after him.

"Doctor, wait!" Amy cried, running down the hallway.

"What is it? What's that noise?" Rory asked, as they found the Doctor outside the TARDIS doors, clearly agitated.

"Oh no, tell me that's not you, old girl, is it?" he muttered nervously, putting an ear up against the blue door. "It _is!_" he said, before pushing open the door and rushing back inside to the controls.

"Feel like explainin' what's going on yet?" Amy asked as she and Rory followed him inside. The Doctor took a moment to answer, still fiddling with switches and buttons in distress. The ringing was much louder now, a deafening alarm in the cavernous control room.

"It's – ah!" the Doctor yelped, as he nudged the wrong lever and a horn sounded. He fixed it, and then leaned, much more cautiously now, against the console. He continued, wearily, "It's the TARDIS's alarm system, sort of a, ah- distress signal." He continued darting about, making tiny adjustments to a million different dials and switches. He finally found the right one and the sound died away. It echoed as it went, ghostly through the long, empty halls of the TARDIS. Rory shivered.

"She's still overheating," the Doctor said. "I just turned the alarm off."

"But you can fix it," Amy said suddenly, in a tone of complete confidence, "If somethin's wrong with the TARDIS…you can fix it. You always do."

But even as the words left her mouth, Amy knew that they were wrong. She could feel it, as she suspected Rory and the Doctor could as well. Something was different this time. This was only confirmed when the Doctor did not answer her, and did not meet her gaze.

The Doctor rubbed his eyes with the heel of his hands. "There's a room," he said, "Somewhere onboard there's a room full of stuff to help me fix the TARDIS. If I can get there, there should be some Arcturan cooling solvent, it'll slow the engine speed, and draw heat away from the controls."

"Oh." Rory said, sounding very surprised, "So that's good then?"

"Yeah, _if_ I can get there," the Doctor said, "and that's a mighty big _if_. Who knows where that room has got to now, I haven't seen it in a couple of centuries, and with the TARDIS in the state she's in…" he trailed off. He put a hand each on Amy and Rory's shoulders.

"Okay, listen. This is the part where I tell you not to follow me. And I know I often say that, but this time, I really mean it. It's very, very dangerous to go wandering about in a faulty TARDIS. Got it?" The Doctor asked, looking very seriously at both of them. Rory and Amy nodded.

"Good." He stood up straight, looking satisfied, and headed out of the control room.

His two companions stood there. Amy looked at Rory. Rory glanced at Amy. And without another word, they both simultaneously followed the Doctor out of the control room, and into the depths of the TARDIS.

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**So did you think this was going to be an alien-planet adventure? Nope! There's going to be lots of in-the-TARDIS shenanigans to come. Hope you enjoyed it. The next chapter will be up soon. Please review, this is only my second fic ever and first Doctor Who one! (I don't know if anyone is a fan of the Leviathan series here, but I recently posted my first fic there, called A World That's Celebrating. It's under a different account but I'm the same person.)**


	2. Chapter 2 - The Doors Disagree

The Doctor looked frustrated when he saw the Ponds were following him, but not particularly surprised.

"Do the words _very dangerous_ mean nothing to you two?" he asked without looking back, although he already knew that the comment was in vain.

"Hm, well, since traveling with you…not really," Amy teased.

The Doctor had to pretend that her remark didn't sting.

He kept walking fast, fast enough that Amy and Rory had to almost jog to catch up. And they were used to the Doctor's fast pace.

They kept going, through endless twisting corridors. Amy thought all of the hallways on the TARDIS would look relatively the same as the hexagonal-shaped ones she'd been in. But they soon left those behind in favor of a stranger walking path.

They went through a low-ceilinged dingy tunnel that looked like it could be a maintenance tunnel modern day London.

They squeezed through a corridor of tiled walls so narrow they had to walk through them sideways, yet the ceiling vanished somewhere high above them.

Sometimes they passed through places that weren't hallways at all, but rather rooms that lead from one to another in a way Amy and Rory would not have thought possible.

They walked around the pool, in the middle of the library. (Though the Doctor was in favor of swimming across to save time. They talked him out of that one by pointing out that he'd get his favorite bow tie all soggy. He reluctantly agreed.)

They went through a room that smelled amazing, stacked floor to ceiling with boxes of tea, all different kinds from all over the universe. Amy made a mental note to try and find this room again the next time they had a slow day.

They walked through a long room lined with marble columns, ending in a few shallow marble steps up to a raised platform. It could have been a throne room, except there was no throne; in fact there was no furniture of any kind at all. All the room had was a small, unmarked door on the far side, through which Rory and Amy were both surprised to find an ordinary closet. They all squeezed inside. The Doctor pushed aside a multitude of tweed blazers and a couple of fur coats to reach a latch, and he pulled down a ladder from the ceiling. They climbed up, and on they went.

They went through at least six laboratories, the med bay, and the console room from which they'd started from at least twice. When this happened, Amy and Rory turned to each other, looking puzzled, but knew better than to ask, the Doctor being in the bad mood he was.

They even passed through Amy's bedroom once, through a door Amy had not previously known was there. At this point Amy started protesting, and was steadfastly ignored.

Rory and Amy started to wish they could have had this tour of the TARDIS when the Doctor was in a better mood. Amy wanted to ask all sorts of questions and hear all his stories, but the Doctor moved relentlessly on in stony silence.

It was around this time that they noticed the TARDIS acting strange. They were hurrying down yet another corridor when a wall appeared in front of them, sealing off the rest of the hallway that had been there. The Doctor looked miffed, but paused hardly a second before barging through a door on the left and taking an alternate route.

This happened three more times.

"So what do you think is going on?" Rory whispered to Amy.

"I've no idea," she whispered back, "But this is _really_ odd."

"You don't…you don't reckon she's doing this on purpose, do you?"

"I don't know. It kind of seems like it, yeah. But why would she do that? I mean, we're trying to fix her."

"I know it doesn't make sense, but that just what it seems like."

The next door hey came across was open. The Doctor, rushing a few paces ahead of them as usual, got there first. When he peered inside he looked angry, and shut the door so quickly he practically slammed it. Amy and Rory jumped. The Doctor just kept going, but this, of course, served only to make Amy desperately curious as to what could possibly be behind that door. She sighed, recognizing that she would probably just have to accept this as yet another mystery about the Doctor.

The door that then appeared in front of them was locked. The Doctor shook the handle and was surprised when it remained closed.

Now, the Doctor knew it was a fundamental part of his relationship with the TARDIS that he respected locked doors. It was more of a symbolic gesture than anything, because both of them knew he could easily just pull out his sonic screwdriver and open it anyway, but if she wanted to close a room, then he would respect her wishes. Usually she only did it for his own good anyway.

But now this door had appeared in front of them, and it was locked, and so were both doors on either side. The Doctor put a hand on the wall beside the door gently.

"Come on, old girl, open up," he coaxed, "I've got to get to the workshop so I can fix you."

A second lock appeared above the first and loudly clicked shut. The Doctor pulled back from the door, looking offended.

"_What? _What's all this about?!" he cried.

The TARDIS did not respond.

"I'm not going back!" the Doctor called, turning away from the door and crossing his arms stubbornly.

The engines whirred indignantly.

"Oh, don't give me any of that," he responded. He stepped forward, resting his forehead against the door. Quietly, he said, "I'm _trying_ to help. But you _have _to _let_ me."

When this garnered no response, he added, "Please don't make me open it." The Doctor slowly took out his sonic screwdriver, looking regretful. The TARDIS suddenly lurched sideways, and they all fell hard to the floor.

Amy and Rory struggled to their feet and the Doctor buzzed open the door, which slammed open with an ear-piercing shriek, and they stormed through.

"I know, I know, I'm sorry!" the Doctor cried, sounding upset and genuinely apologetic. "Please don't, I… I had to. It's for your own good. .."

At this point, Amy, seeing that the Doctor seemed inclined to stay there and keep apologizing to the door, interrupted him.

"Doctor! Let's just… keep going, yeah?" she finished hesitantly, seeing the saddened look he gave her. But he followed her advice, and, resuming his previous stony silence, continued onward down the corridor.

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**Thanks for reading! Review, maybe? Next chapter will be coming shortly.**

**Also, thanks to madmanwithascrewdriver for beta reading!**

**Disclaimer: I don't own Doctor Who.**


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